In the episode, "Two Ships," when two airplanes collided and crashed in downtown Chicago, Dr. Gates and Dr. Rasgotra again worked together, this time out in the field.

It was revealed that Tony had a girlfriend named Meg who was using her deceased husband's life insurance money to get him through medical school.

Despite everyone's best efforts, Meg eventually died from an intentional overdose of medication, leaving Tony flooded with guilt and holding Sarah by his side.

More of Gates's life is exposed when he allows his father, an alcoholic ex-fireman played by Stacy Keach, to move in with him and Sarah.

Tony begins thinking about legal intervention after speaking with his lawyer about Sarah, who wants to stay with him regardless of her grandparents' wishes.

However, at the end of the season, Meg's parents show up with legal documents and take Sarah without talking to Tony, saying this will make for an easier transition.

Later, the grandfather of a young girl who died from injuries sustained during the stampede strangled the jerk to death, having realized who he was as a result of Gates's actions.

Sarah's grandmother later got angry with him when he wanted her husband to have surgery after a heart episode, though they eventually mended fences and Gates then said they should go with a different option presented by Dr. Morris.

After Gates called Sam for being distant towards him, they began a more mature dating relationship, although they also got caught having sex on a hospital security camera.

Tony and the interns are forced to remain quarantined in the exam room as Banfield, Archie Morris, Samantha Taggart and Neela Rasgotra help evacuate.